From what I have read yes, it is possible and it a lot more prevalent than you would think. Perhaps not all the way through the RPM range, but at certain areas yes. I've seen some people claim achieving this with LS engines.
I used to race in a drag boat class that had the same rules as NHRA Pro Stock (500 ci N/A). I acheived 127% VE at certain areas in the rpm range. This was back in the early 90s. I'm sure that technology has come so far that it is probably higher today in many racing engines.
You need to understand that air is a fluid, and when you get to maximum efficieny, which is max torque, the air flowing into the intake manifold doesn't stop moving just because the intake valve closes. So when the valve closes, there is a pressure wave behind the valve that is higher than atmospheric conditions and as soon as the valve opens, you can get a pressurized charge.
its all about the flow dynamics, and tuning so that a certain rpm will use the pressure waves to maximize flow into the cyl and exhausst scavenging. great for a race car that sits around the same rpm for a long time, but hard to really use on a street car.
Here is my dyno chart from my L92 headed 402, This dynosheet was generated on a superflow 902 water-brake dyno and reflects FWHP, we had a precision flow meter installed to measure actual airflow and build the VE chart in HP-tuners.
__________________ 01 Z-28 M6, HP Tuners.
LS-2 402 - L92/L76 in process.....
Its absolutely possible and happens on lots of vehicles, cant really say for sure on how many but it is common. It comes from velocity of the air actually filling the cylinder more than the cylinder could have filled its self. Once you get that air moving so fast through the engine it wants to keep going, so at some points it actually rams into the cylinder and overfills it giving you over 100% VE.
And yes its from scavenging, that occurs during overlap. That is when both intake and exhaust valves are open at the same time and air is allowed to flow through the intake into the cylinder and out the exhaust, at some point that flow gets moving so well that when the exh valve closes and the intake is still open the air keeps flowing in with velocity behind it and there it is 100+ VE
For instance the cams with lower LSA give you more overlap, and that works both positively and negatively depending on what your goal is and where you use it. At higher RPM it gives you more scavenging but low RPM it gives you an adverse affect and a rough idle. It also plays a role into power band etc etc etc etc... cams are complicated and so it this discussion lol.
Thats my laymans term description after a few beers hope it makes sense
I dont know if you can actually figure VE, you can measure it though, but thats getting beyond my understanding of it all.
__________________ 2000 SS A4 HARDTOP, Fikse FM5 17x9.5 & 17x11, Eibach prokit, Edelbrock adj panhard, LCA's, LCA relocation brackets, Ported TB, Yank PYE3400, LS6 Intake, Hooker long tubes, Lane's True Duals, Tune, LS6 heads and some valve train stuff to put on, cam coming eventually.
The graph I posted on my 402 was with some 1-7/8" American Racing F-body Headers that have a nice merge collector with a "velocity spike". It actually showed a significant gain in the touque output and VE over the 1 -7/8" dyno headers we started with when I dynoed. If I get a chance I should plot them one over the other, it would be interesting. Kurt
__________________ 01 Z-28 M6, HP Tuners.
LS-2 402 - L92/L76 in process.....
There are alot of ways to achieve a VE of 100+. For example cam design plays apart by creating vacume using ramp speed and overlap. The intake port itself plays a huge roll buy creating port velocity speeds great enough to force the air keep filling the cylinder even when the air pressure in the cylinder is greater than out side. Another way is Intake runner design using the air's natural want to ossicilate back and forth to create pressure at optimun time when Intake Valve Open occurs to give a supercharging effect. Ferrari Does this alot. So yes a VE of >100% can be achieved not extreamly easily but is possible.
Is more that 100% VE possible without FI? 
